The source code for building the mkhssp and hsspconv
programs is bundled in the hssp project. The mkhssp executable
creates stockholm files with hssp annotations in them. The hsspconv
executable converts stockholm to the original hssp format.
Development
The provided Dockerfile sets up a development environment. Build the docker
image using the command docker build -t hssp . and run the image in a
container, with a local source copy and data files mounted, with the command
docker run -v /home/jon/projects/hssp:/app -v /mnt/extra:/srv/data -it hssp.
Download and installation instructions
Source code archives are available here.
Compiling hssp programs
Pre-requisites
Compiler:
- Must support at least the c++ 11 standard.
System libraries:
- libzeep version >= 3.0 (for mkhssp --fetch-dbrefs only)
- libboost version >= 1.48
- libz
- libbz2
- autoconf
- automake
- autotools-dev
Instructions
Download and uncompress the hssp source code archive (version >= 2.2.6):
wget https://github.com/cmbi/hssp/archive/hssp-?.?.?.tar.gz
tar -zxvf hssp-?.?.?.tar.gz
cd hssp-?.?.?
Configure and build the hssp executables:
./autogen.sh
./configure
make
To build only one executable of the hssp project, e.g. mkhssp, type:
make mkhssp
To test the mkhssp executable type:
./mkhssp
To add the executables to /usr/local/bin type:
sudo make install
Citing hssp
The reference for the new versions of hssp and other protein structure bioinformatics facilities is:
A series of PDB-related databanks for everyday needs
Wouter G. Touw, Coos Baakman, Jon Black, Tim A. H. te Beek,
E. Krieger, Robbie P. Joosten and Gert Vriend.
Nucl. Acids Res. (2015) 43, D364-D368
The original reference for DSSP is:
Dictionary of protein secondary structure: pattern recognition of
hydrogen-bonded and geometrical features.
Kabsch W and Sander C, Biopolymers (1983) 22, 2577-2637.
The original reference for HSSP is:
Database of homology-derived protein structures and the structural
meaning of sequence alignment.
Sander C and Schneider R, Proteins (1991) 9, 56-68.
Contact
In 2013, maintenance of hssp has been taken over from Maarten Hekkelman by Coos Baakman. If you want to provide feedback, either send an e-mail to hssp.cmbi@radboudumc.nl or have a look at existing issues (if necessary, create a new issue).
